# Data wrangling
library(tidyverse)
# Plotting
library(cowplot)
library(plotly)
library(factoextra)
source('/home/jin/OneDrive/SGB/projects/functions.R')
This is where I would write a summary about the study/project - i.e. how it came about, who is involved, research question, what types of data were delivered, etc.
For the demo, we’ll just use the mtcars dataset.
mtcars
Output from plotting functions are included.
mtcars %>%
select(mpg, cyl, disp, hp) %>%
rownames_to_column(var='Model') %>%
pivot_longer(cols=-Model) %>%
ggplot(mapping=aes(x=Model,value)) +
geom_bar(stat='identity') +
facet_grid(name ~ ., scales='free') +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
For .html output, you can include 3D interactive plots using
plotly package.
res.pca <- prcomp(mtcars)
fviz_pca_ind(res.pca,
col.ind=as.factor(mtcars$cyl),
addEllipses = TRUE,
legend.title='cyl',
repel=TRUE,
title='')
plotly_pca(res.pca, as.factor(mtcars$cyl))
.tocify-header {
text-indent: initial;
}
.tocify-subheader > .tocify-item {
text-indent: initial;
padding-left: 20px;
}
.tocify-subheader .tocify-subheader > .tocify-item {
text-indent: initial;
padding-left: 30px;
}
.tocify-subheader .tocify-subheader .tocify-subheader > .tocify-item {
text-indent: initial;
padding-left: 40px;
}
.tocify-subheader .tocify-subheader .tocify-subheader > .tocify-item {
text-indent: initial;
padding-left: 50px;
}
knitr::opts_chunk$set(
echo = TRUE,
include = TRUE,
cache = FALSE,
dpi = 150,
cache.lazy = FALSE
)
# Data wrangling
library(tidyverse)
# Plotting
library(cowplot)
library(plotly)
library(factoextra)
source('/home/jin/OneDrive/SGB/projects/functions.R')
mtcars
mtcars %>%
select(mpg, cyl, disp, hp) %>%
rownames_to_column(var='Model') %>%
pivot_longer(cols=-Model) %>%
ggplot(mapping=aes(x=Model,value)) +
geom_bar(stat='identity') +
facet_grid(name ~ ., scales='free') +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
res.pca <- prcomp(mtcars)
fviz_pca_ind(res.pca,
col.ind=as.factor(mtcars$cyl),
addEllipses = TRUE,
legend.title='cyl',
repel=TRUE,
title='')
plotly_pca(res.pca, as.factor(mtcars$cyl))
sessionInfo()
sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Stream 9
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.15.so
##
## locale:
## [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8
## [4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
## [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] officer_0.4.3 officedown_0.2.4 factoextra_1.0.7 plotly_4.10.0 cowplot_1.1.1
## [6] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
## [11] tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2 DT_0.23
##
## loaded via a namespace (and not attached):
## [1] fs_1.5.2 lubridate_1.8.0 httr_1.4.3 rprojroot_2.0.3
## [5] tools_4.1.3 backports_1.4.1 bslib_0.4.0 utf8_1.2.2
## [9] R6_2.5.1 lazyeval_0.2.2 DBI_1.1.3 colorspace_2.0-3
## [13] withr_2.5.0 tidyselect_1.1.2 prettyunits_1.1.1 processx_3.7.0
## [17] curl_4.3.2 compiler_4.1.3 cli_3.3.0 rvest_1.0.2
## [21] xml2_1.3.3 labeling_0.4.2 sass_0.4.2 scales_1.2.0
## [25] callr_3.7.1 systemfonts_1.0.4 digest_0.6.29 rmarkdown_2.14
## [29] pkgconfig_2.0.3 htmltools_0.5.3 dbplyr_2.2.1 fastmap_1.1.0
## [33] highr_0.9 rvg_0.2.5 htmlwidgets_1.5.4 rlang_1.0.4
## [37] readxl_1.4.0 rstudioapi_0.13 xaringan_0.27 farver_2.1.1
## [41] jquerylib_0.1.4 generics_0.1.3 jsonlite_1.8.0 crosstalk_1.2.0
## [45] zip_2.2.0 car_3.1-0 googlesheets4_1.0.0 magrittr_2.0.3
## [49] Rcpp_1.0.9 munsell_0.5.0 fansi_1.0.3 gdtools_0.2.4
## [53] abind_1.4-5 lifecycle_1.0.1 stringi_1.7.8 yaml_2.3.5
## [57] carData_3.0-5 pkgbuild_1.3.1 grid_4.1.3 ggrepel_0.9.1
## [61] promises_1.2.0.1 crayon_1.5.1 haven_2.5.0 hms_1.1.1
## [65] knitr_1.39 ps_1.7.1 pillar_1.8.0 uuid_1.1-0
## [69] ggpubr_0.4.0 ggsignif_0.6.3 reprex_2.0.1 servr_0.25
## [73] glue_1.6.2 evaluate_0.15 data.table_1.14.2 remotes_2.4.2
## [77] modelr_0.1.8 vctrs_0.4.1 tzdb_0.3.0 httpuv_1.6.5
## [81] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 cachem_1.0.6
## [85] xfun_0.31 mime_0.12 broom_1.0.0 rstatix_0.7.0
## [89] later_1.3.0 viridisLite_0.4.0 googledrive_2.0.0 gargle_1.2.0
## [93] memoise_2.0.1 ellipsis_0.3.2